applicativesystem

Finished writing the code and had no access to internet since morning and hence pushing it now. Final and binary release.

Cargo.toml

@@ -0,0 +1,7 @@
+[package]
+name = "rust-lcp-arrays"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+clap = { version = "4.5.23", features = ["derive"] }

README.md

@@ -1,2 +1,31 @@
-# rust-suffix-lcp-arrays
- rust suffix lcp arrays 
+# rust-lcp-arrays
+
+ - rust lcp arrays 
+ - kasai algorithm says that use a inverse suffix tree but that is cost consuming.Instead, i implemented a string compression way so that it estimates the proportion of the
+match based on the ith offset for the i+1 offset.
+ - general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.
+
+
+ ```
+ cargo build 
+ 
+ ```
+ ```
+➜ gauravsablok  rust-suffix-lcp git:(main) ✗ ./target/debug/rust-lcp-arrays -h
+Usage: rust-lcp-arrays <LCPARRAY_ARG>
+
+Arguments:
+  <LCPARRAY_ARG>  please provide the path to the fastq file
+
+Options:
+  -h, --help     Print help
+  -V, --version  Print version
+```
+- to run the binary 
+```
+./rust-lcp-arrays ./sample-files/sample.fasta
+{[28, 19, 24, 15, 11, 7, 21, 4, 0, 20, 3, 25, 16, 12, 8, 27, 18, 23, 14, 10, 6, 2, 26, 17, 22, 13, 9, 5, 1]: LCPArray { suffixindex: [28, 19, 24, 15, 11, 7, 21, 4, 0, 20, 3, 25, 16, 12, 8, 27, 18, 23, 14, 10, 6, 2, 26, 17, 22, 13, 9, 5, 1], suffixarray: ["A", "ACATGACTGA", "ACTGA", "ACTGACATGACTGA", "ACTGACTGACATGACTGA", "ACTGACTGACTGACATGACTGA", "ATGACTGA", "ATGACTGACTGACTGACATGACTGA", "ATGCATGACTGACTGACTGACATGACTGA", "CATGACTGA", "CATGACTGACTGACTGACATGACTGA", "CTGA", "CTGACATGACTGA", "CTGACTGACATGACTGA", "CTGACTGACTGACATGACTGA", "GA", "GACATGACTGA", "GACTGA", "GACTGACATGACTGA", "GACTGACTGACATGACTGA", "GACTGACTGACTGACATGACTGA", "GCATGACTGACTGACTGACATGACTGA", "TGA", "TGACATGACTGA", "TGACTGA", "TGACTGACATGACTGA", "TGACTGACTGACATGACTGA", "TGACTGACTGACTGACATGACTGA", "TGCATGACTGACTGACTGACATGACTGA"], lcparray: [1, 0, 5, 0, 0, 0, 8, 0, 0, 9, 0, 4, 0, 0, 0, 2, 0, 6, 0, 0, 0, 0, 3, 0, 7, 0, 0, 0, 0] }}
+
+```
+
+ Gaurav Sablok 

sample-files/lcp-array.txt

@@ -0,0 +1,2 @@
+[28, 19, 24, 15, 11, 7, 21, 4, 0, 20, 3, 25, 16, 12, 8, 27, 18, 23, 14, 10, 6, 2, 26, 17, 22, 13, 9, 5, 1]	[28, 19, 24, 15, 11, 7, 21, 4, 0, 20, 3, 25, 16, 12, 8, 27, 18, 23, 14, 10, 6, 2, 26, 17, 22, 13, 9, 5, 1]	["A", "ACATGACTGA", "ACTGA", "ACTGACATGACTGA", "ACTGACTGACATGACTGA", "ACTGACTGACTGACATGACTGA", "ATGACTGA", "ATGACTGACTGACTGACATGACTGA", "ATGCATGACTGACTGACTGACATGACTGA", "CATGACTGA", "CATGACTGACTGACTGACATGACTGA", "CTGA", "CTGACATGACTGA", "CTGACTGACATGACTGA", "CTGACTGACTGACATGACTGA", "GA", "GACATGACTGA", "GACTGA", "GACTGACATGACTGA", "GACTGACTGACATGACTGA", "GACTGACTGACTGACATGACTGA", "GCATGACTGACTGACTGACATGACTGA", "TGA", "TGACATGACTGA", "TGACTGA", "TGACTGACATGACTGA", "TGACTGACTGACATGACTGA", "TGACTGACTGACTGACATGACTGA", "TGCATGACTGACTGACTGACATGACTGA"]	[1, 0, 5, 0, 0, 0, 8, 0, 0, 9, 0, 4, 0, 0, 0, 2, 0, 6, 0, 0, 0, 0, 3, 0, 7, 0, 0, 0, 0]
+

sample-files/sample.fasta

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+@samplefasta
+ATGCATGACTGACTGACTGACATGACTGA

src/args.rs

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+use clap::Parser;
+
+#[derive(Debug, Parser)]
+#[clap(version)]
+
+pub struct LCPArraysArgs {
+    /// please provide the path to the fastq file
+    pub lcparray_arg: String
+}